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!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6621 ECOCYC:G6621]
EcoCyc:G6621
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
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[http://ecogene.org/geneinfo.php?eg_id=EG13898 EcoGene:EG13898]
EcoGene:EG13898
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[RegulonDB]]
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RegulonDB:ECK120003216
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:EB3657
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[ASAP]]
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ASAP:ABE-0004002
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Revision as of 07:13, 27 May 2013

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

ldcA

Mnemonic

L,D-carboxypeptidase A

Synonyms

ECK1180, b1192, JW1181, ycgQ[1], ycgQ

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

26.76 minutes 

MG1655: 1242303..1241389
<gbrowseImage> name=NC_000913:1241389..1242303 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1243230..1242316
<gbrowseImage> name=NC_012967:1242316..1243230 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1130110..1131024
<gbrowseImage> name=NC_012759:1130110..1131024 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1244657..1243743
<gbrowseImage> name=AC_000091:1243743..1244657 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1282544..1281630
<gbrowseImage> name=NC_010473:1281630..1282544 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔldcA (Keio:JW1181)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9086[3]

ΔldcA::kan

deletion

Biolog:respiration

unable to respire b-Methyl-D-glucoside

PMID:16095938[4]

ΔldcA::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[4]

ΔldcA::kan

deletion

Biolog:respiration

unable to respire a-Hydroxybutyrate

PMID:16095938[4]

ΔldcA::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938[4]

ΔldcA::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[4]

ΔldcA::kan

deletion

Biolog:respiration

unable to respire Succinate

PMID:16095938[4]

ΔldcA::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938[4]

ΔldcA::kan

deletion

Biolog:respiration

unable to respire L-Alanine

PMID:16095938[4]

ΔldcA::kan

deletion

Biolog:respiration

unable to respire L-Alanyl-glycine

PMID:16095938[4]

ΔldcA::kan

deletion

Biolog:respiration

unable to respire L-Asparagine

PMID:16095938[4]

ΔldcA::kan

deletion

Biolog:respiration

unable to respire L-Aspartate

PMID:16095938[4]

ΔldcA::kan

deletion

Biolog:respiration

unable to respire Glycyl-L-aspartate

PMID:16095938[4]

ΔldcA::kan

deletion

Biolog:respiration

unable to respire D-Serine

PMID:16095938[4]

ΔldcA::kan

deletion

Biolog:respiration

unable to respire L-Serine

PMID:16095938[4]

ΔldcA782::kan

PMID:16738554[2]

CGSC:101640

ldcA782(del)::FRTKanFRT

Sensitivity to

Increase sensitivity to UV.

PMID:23224554[5]

Experimental Strain: SMR12050

Parental strain: SMR4562

See Table S1 & S7

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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW1181

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCTCTCTGTTTCACTTAATTGC

Primer 2:CCCATTTTAAGAACAGGATGACC

11G8

Kohara Phage

Genobase

PMID:3038334[7]

7C10

Kohara Phage

Genobase

PMID:3038334[7]

fadR13::Tn10

Linked marker

CAG18497 = CGSC7365[3]

est. P1 cotransduction: 78% [8]

oppC506::Tn10

Linked marker

CAG12169 = CGSC7369[3]

est. P1 cotransduction: 4% [8]
Synonyms:zch-506::Tn10, zci-506::Tn10

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:G6621

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13898

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945756

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003216

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3657

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004002

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.00 4.01 4.02 4.03 4.04 4.05 4.06 4.07 4.08 4.09 4.10 4.11 4.12 4.13 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  5. ↑ Al Mamun, AA et al. (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338 1344-8 PubMed
  6. ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  7. ↑ 7.0 7.1 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  8. ↑ 8.0 8.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

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